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OliverWoollandOliverWoolland
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Merge pull request #16 from eScienceLab/development
Update portal with branding
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‎.docker/deployment/domain_change.sh‎

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docker_address="http://host.docker.internal:3030/rocrate/sparql"
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local_address="http://localhost:3030/rocrate/sparql"
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server_address="https://query.ro-crate.org/rocrate/sparql"
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files=( "src/configs/rocrate/search_perspectives/profiles.json"
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"src/configs/portalConfig.json" )
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for file in ${files[@]}; do
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sed -e "s|${docker_address}|${server_address}|g" \
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-e "s|${local_address}|${server_address}|g" ${file} > ${file}.temp
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mv ${file}.temp $file
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done

‎.docker/fuseki/config.ttl‎

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# Licensed under the terms of http://www.apache.org/licenses/LICENSE-2.0
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## Fuseki Server configuration file.
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@prefix : <#> .
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@prefix fuseki: <http://jena.apache.org/fuseki#> .
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@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
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@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
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@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
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@prefix tdb2: <http://jena.apache.org/2016/tdb#> .
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@prefix text: <http://jena.apache.org/text#> .
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@prefix ja: <http://jena.hpl.hp.com/2005/11/Assembler#> .
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@prefix crm: <http://www.cidoc-crm.org/cidoc-crm/> .
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@prefix ns11: <http://schema.org/> .
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[] rdf:type fuseki:Server ;
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# Example::
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# Server-wide query timeout.
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#
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# Timeout - server-wide default: milliseconds.
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# Format 1: "1000" -- 1 second timeout
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# Format 2: "10000,60000" -- 10s timeout to first result,
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# then 60s timeout for the rest of query.
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#
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# See javadoc for ARQ.queryTimeout for details.
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# This can also be set on a per dataset basis in the dataset assembler.
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#
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# ja:context [ ja:cxtName "arq:queryTimeout" ; ja:cxtValue "30000" ] ;
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# Add any custom classes you want to load.
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# Must have a "public static void init()" method.
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# ja:loadClass "your.code.Class" ;
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fuseki:services (
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[ rdf:type fuseki:Service ;
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fuseki:name "rocrate" ;
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fuseki:serviceQuery "sparql" ;
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fuseki:serviceUpdate "update" ;
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fuseki:serviceUpload "upload" ;
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fuseki:serviceReadWriteGraphStore "data" ;
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fuseki:dataset :text_dataset ;
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]
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)
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# End triples.
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.
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## RO-Crate
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:text_dataset rdf:type text:TextDataset ;
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text:dataset :tdb_dataset ;
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text:index <#indexLucene> ;
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.
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:tdb_dataset rdf:type tdb2:DatasetTDB2 ;
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tdb2:location "/fuseki/databases/rocrate" ;
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tdb2:unionDefaultGraph false ; # true: default graph becomes a union of all named graphs
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.
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<#indexLucene> a text:TextIndexLucene ;
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text:directory <file:/fuseki/run/databases/rocrate_index> ;
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text:entityMap <#entMap> ;
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.
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<#entMap> a text:EntityMap ;
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text:defaultField "text" ;
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text:entityField "uri" ;
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text:map (
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[ text:field "text" ; text:predicate rdfs:label ]
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[ text:field "text" ; text:predicate skos:prefLabel ]
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[ text:field "text" ; text:predicate ns11:name ]
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)
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.

‎.docker/sampo-ui/deploy.dockerfile‎

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FROM node:16.13.0-alpine
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ARG API_URL
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ARG VERSION="3.0.0"
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# Based on https://nodejs.org/en/docs/guides/nodejs-docker-webapp/
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# Create app directory
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WORKDIR /usr/src/app
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# Download Sampo UI from GitHub and unzip
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# mv commands: install app dependencies, Babel 7 presets and plugins, and bundle app source
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# Remove redundant files
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RUN <<EOF
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wget https://github.com/SemanticComputing/sampo-ui/archive/refs/tags/v$VERSION.zip
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unzip v$VERSION.zip
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mv ./sampo-ui-$VERSION/package*.json ./
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mv ./sampo-ui-$VERSION/webpack*.js ./
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mv ./sampo-ui-$VERSION/babel.config.js ./
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mv ./sampo-ui-$VERSION/src ./src
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rm -rf sampo-ui-$VERSION v$VERSION.zip
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EOF
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COPY ./src ./src
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# Run the scripts defined in package.json using build arguments
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RUN npm install && \
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API_URL=$API_URL npm run build
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EXPOSE 3001
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# https://github.com/nodejs/docker-node/blob/main/docs/BestPractices.md#non-root-user
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USER node
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# Express server handles the backend functionality and also serves the React app
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CMD ["node", "/usr/src/app/dist/server"]

‎.docker/sampo-ui/dev.dockerfile‎

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FROM node:16.13.0-alpine
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# Specify the Sampo UI version
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ARG VERSION="3.0.0"
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RUN apk update && apk add bash
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# Create app directory
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WORKDIR /usr/src/app
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# Download Sampo UI from GitHub and unzip
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# mv commands: install app dependencies, Babel 7 presets and plugins, and bundle app source
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# Remove redundant files
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RUN <<EOF
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wget https://github.com/SemanticComputing/sampo-ui/archive/refs/tags/v$VERSION.zip
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unzip v$VERSION.zip
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mv ./sampo-ui-$VERSION/package*.json ./
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mv ./sampo-ui-$VERSION/webpack*.js ./
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mv ./sampo-ui-$VERSION/babel.config.js ./
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mv ./sampo-ui-$VERSION/src ./src
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rm -rf sampo-ui-$VERSION v$VERSION.zip
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EOF
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# Run the scripts defined in package.json using build arguments
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RUN npm install
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# Install nodemon
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RUN npm install -g nodemon
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EXPOSE 8080 3001
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# https://github.com/nodejs/docker-node/blob/main/docs/BestPractices.md#non-root-user
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USER node
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# Run dev server
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CMD ["npm", "run", "dev"]

‎.github/workflows/deploy.yml‎

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name: Deploy to Remote (Self-Hosted)
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on:
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push:
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branches:
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- main
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workflow_dispatch:
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jobs:
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deploy:
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name: Docker Compose Up
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runs-on: self-hosted
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steps:
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- name: Checkout repo
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uses: actions/checkout@v3
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- name: Change domain paths
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run: bash .docker/deployment/domain_change.sh
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- name: Generate .env from template
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env:
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ENV_FUSEKI_PASSWORD: ${{ secrets.ENV_FUSEKI_PASSWORD }}
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ENV_SAMPO_API_URL: ${{ vars.ENV_SAMPO_API_URL }}
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run: |
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envsubst < env.template > .env
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- name: Clean up Docker compose
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run: |
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docker compose -f docker-compose.deploy.yml down
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- name: Deploy with Docker Compose
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run: |
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docker compose -f docker-compose.deploy.yml pull
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docker compose -f docker-compose.deploy.yml up -d --build

‎.gitignore‎

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# Environments
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.env

‎CODEOWNERS‎

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@AnnieZQH
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@OliverWoolland
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@elichad
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@stain

‎Caddyfile‎

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profiles.ro-crate.org {
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reverse_proxy sampo-dashboard:3001
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}
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query.ro-crate.org {
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reverse_proxy jena-fuseki:3030
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}

‎README.md‎

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# sampo-dashboard
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# RO-Crate Profile Portal
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## About
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RO-Crates are a method for packaging research data with their metadata. RO-Crate Profiles define the conventions, types and properties to do this for specific communities and domains.
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## Submitting a profile to the portal
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The profile portal is accepting contributions!
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> [!IMPORTANT]
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> To be accepted, the profile must be a [Profile Crate](url) accessible on the public internet.
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To add your profile (or a profile you feel is missing):
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- Open `scripts/profile_urls.txt` in this repo for editing (click file, then click pencil icon)
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- Append the URL of your profile to the file on a new line
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- Click `Commit Changes` and select `Create a new branch for this commit and start a pull request`
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- In the `Open a pull request window`, click `Create pull request` - the RO-Crate team will now be notified about your request
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- When the pull request page has opened, you will notice some automated checks running
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- :white_check_mark: If successful: all good, the team will review and merge your request
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- :x: If the check fails: there is an error or problem with your URL, either click the link to view the error message and debug or [raise a ticket for the RO-Crate team here](https://github.com/eScienceLab/sampo-dashboard/issues)
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## Development Setup
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### 1. Clone the repository
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To clone the [repository](https://github.com/eScienceLab/sampo-dashboard), click `<> Code` above the list of files on the GitHub page of this repo, and copy the URL under your choice of clone method (HTTPS / SSH Key / GitHub CLI).
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In the CLI: \
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`git clone <URL>`
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Change into the project directory for the following steps: \
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`cd sampo-dashboard`
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### 2. Configure .env
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Make a copy of `env.template`, rename it to `.env` and populate the variables.
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### 3. Build Docker images and start containers
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The following command builds the development Docker images (`--build`) before starting containers in detached mode (`-d`).
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`docker compose -f docker-compose.dev.yml up -d --build`
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### 4. Stop and remove containers and networks
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`docker compose -f docker-compose.dev.yml down`

‎docker-compose.deploy.yml‎

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services:
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caddy:
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image: caddy:2.10
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container_name: caddy
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restart: unless-stopped
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ports:
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- 80:80
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- 443:443
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volumes:
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- ./Caddyfile:/etc/caddy/Caddyfile:ro
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- caddy-config:/config
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networks:
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- web-network
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sampo-dashboard:
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container_name: rocrate-sampo-dashboard
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build:
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context: .
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dockerfile: .docker/sampo-ui/deploy.dockerfile
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args:
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API_URL: ${SAMPO_API_URL}
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# image: ghcr.io/esciencelab/sampo-dashboard
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# platform: ${DOCKER_DEFAULT_PLATFORM:-linux/x86_64}
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restart: unless-stopped
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tty: true
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networks:
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- web-network
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ports:
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- "3006:3001"
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volumes:
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- node_modules:/usr/src/app/node_modules/
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jena-fuseki:
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container_name: rocrate-jena-fuseki
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image: stain/jena-fuseki
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platform: ${DOCKER_DEFAULT_PLATFORM:-linux/x86_64}
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restart: unless-stopped
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tty: true
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networks:
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- web-network
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ports:
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- "3030:3030"
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volumes:
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- jena-fuseki-data:/fuseki
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- ./.docker/fuseki/config.ttl:/fuseki/config.ttl
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environment:
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ADMIN_PASSWORD: ${FUSEKI_PASSWORD}
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networks:
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web-network:
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name: rocrate-web-network
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volumes:
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jena-fuseki-data:
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name: rocrate-data
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node_modules:
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name: rocrate-node_modules
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caddy-config:

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